Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada.
PLoS One. 2019 Jul 24;14(7):e0219961. doi: 10.1371/journal.pone.0219961. eCollection 2019.
Pathogen monitoring, detection and removal are essential to public health and outbreak management. Systems are in place for monitoring the microbial load of hospitals and public health facilities with strategies to mitigate pathogen spread. However, no such strategies are in place for ambulances, which are tasked with transporting at-risk individuals in immunocompromised states. As standard culturing techniques require a laboratory setting, and are time consuming and labour intensive, our approach was designed to be portable, inexpensive and easy to use based on the MinION third-generation sequencing platform from Oxford Nanopore Technologies. We developed a transferable sampling-to-analysis pipeline to characterize the microbial community in emergency medical service vehicles. Our approach identified over sixty-eight organisms in ambulances to the genera level, with a proportion of these being connected with health-care associated infections, such as Clostridium spp. and Staphylococcus spp. We also monitored the microbiome of different locations across three ambulances over time, and examined the dynamic community of microorganisms found in emergency medical service vehicles. Observed differences identified hot spots, which may require heightened monitoring and extensive cleaning. Through metagenomics analysis it is also possible to identify how microorganisms spread between patients and colonize an ambulance over time. The sequencing results aid in the development of practices to mitigate disease spread, while also providing a useful tool for outbreak prediction through ongoing analysis of the ambulance microbiome to identify new and emerging pathogens. Overall, this pipeline allows for the tracking and monitoring of pathogenic microorganisms of epidemiological interest, including those related to health-care associated infections.
病原体监测、检测和清除对于公共卫生和疫情管理至关重要。已经建立了医院和公共卫生设施微生物负荷监测系统，以制定减轻病原体传播的策略。然而，对于负责运送免疫功能低下的高危个体的救护车，却没有这样的策略。由于标准的培养技术需要实验室环境，且耗时费力，我们的方法旨在基于牛津纳米孔技术的 MinION 第三代测序平台，具有便携性、低成本和易于使用的特点。我们开发了一种可转移的采样分析管道，以表征紧急医疗服务车辆中的微生物群落。我们的方法能够鉴定出救护车中 68 多种生物体到属的水平，其中一些与与医疗保健相关的感染有关，如梭状芽孢杆菌和葡萄球菌。我们还监测了三辆救护车不同位置随时间的微生物组，并检查了紧急医疗服务车辆中发现的微生物群落的动态。观察到的差异确定了热点，这些热点可能需要加强监测和广泛清洁。通过宏基因组学分析，还可以确定微生物如何在患者之间传播并随时间在救护车上定植。测序结果有助于制定减轻疾病传播的措施，同时通过持续分析救护车微生物组来识别新出现的病原体，为疫情预测提供有用的工具。总体而言，该管道允许对包括与医疗保健相关感染相关的具有流行病学意义的致病微生物进行跟踪和监测。
